Skip to content

max_index #312

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
davidmeunier79 merged 18 commits into from
Jul 30, 2025
Merged

max_index #312

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
18 commits
Select commit Hold shift + click to select a range
880e949
max_index
davidmeunier79 Jul 16, 2025
24c2b27
Merge branch 'master' into modif_average_align
davidmeunier79 Jul 16, 2025
a75cb25
print
davidmeunier79 Jul 16, 2025
8692057
better modifier on noseg and prep
davidmeunier79 Jul 23, 2025
c8d12d3
4animal
davidmeunier79 Jul 23, 2025
f885b55
use_T2 error in prepare
davidmeunier79 Jul 23, 2025
36c5d94
if erode/dilate
davidmeunier79 Jul 24, 2025
41d3cd9
IsoSurface_tissues_pipe
davidmeunier79 Jul 24, 2025
f0799d6
if erode/dilate else gcc only
davidmeunier79 Jul 24, 2025
a1c17a8
gm
davidmeunier79 Jul 24, 2025
3137f76
itk_debias export mask
davidmeunier79 Jul 25, 2025
0f3767f
flake8
davidmeunier79 Jul 28, 2025
5499c5c
keep_gcc_by_index before
davidmeunier79 Jul 28, 2025
8f8d8a7
keep_gcc_by_index
davidmeunier79 Jul 28, 2025
a74f19f
back to keep_gcc in wmgm (otherwise issues with csf and sub tissues)
davidmeunier79 Jul 28, 2025
2307da1
using stereoINT template as well
davidmeunier79 Jul 29, 2025
c38e898
1_6seg_stereoINT
davidmeunier79 Jul 29, 2025
a880a4e
tissues
davidmeunier79 Jul 30, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion macapype/nodes/correct_bias.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -258,4 +258,4 @@ def itk_debias(img_file):
mask_img_file = os.path.abspath(fname + "_mask" + ext)
sitk.WriteImage(input_image_mask, mask_img_file)

return cor_img_file, bias_img_file
return cor_img_file, bias_img_file, mask_img_file
13 changes: 11 additions & 2 deletions macapype/nodes/prepare.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,7 @@ def _list_outputs(self):

###############################################################################
# Equivalent of flirt_average in FSL
def average_align(list_img, reorient=False):
def average_align(list_img, reorient=False, max_index=None):

import os
import nibabel as nib
Expand All @@ -299,7 +299,16 @@ def average_align(list_img, reorient=False):
data_0_shape = data_0.shape
list_data = [data_0]

for i, img in enumerate(list_img[1:]):
if max_index is not None:
assert max_index < len(list_img), f"Error with {max_index=}"

for i, img in enumerate(list_img[1:], 1):

if max_index is not None:
if i > max_index:
print(f"Iter {i=} higher than {max_index=}")
continue

data_orig_shape = nib.load(img).get_fdata().shape
if data_orig_shape != data_0_shape:
print(f"**** Warning , original image shape \
Expand Down
121 changes: 92 additions & 29 deletions macapype/pipelines/prepare.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -588,13 +588,25 @@ def create_short_preparation_pipe(params, params_template={},
N4debias_T2, "indiv_params")

# outputnode
data_preparation_pipe.connect(
N4debias_T1, "output_image",
outputnode, "stereo_debiased_T1")
if "use_T2" in params.keys():

data_preparation_pipe.connect(
N4debias_T2, "output_image",
outputnode, "stereo_debiased_T2")
data_preparation_pipe.connect(
N4debias_T1, "output_image",
outputnode, "stereo_debiased_T2")

data_preparation_pipe.connect(
N4debias_T2, "output_image",
outputnode, "stereo_debiased_T1")

else:

data_preparation_pipe.connect(
N4debias_T1, "output_image",
outputnode, "stereo_debiased_T1")

data_preparation_pipe.connect(
N4debias_T2, "output_image",
outputnode, "stereo_debiased_T2")

elif "fast" in params.keys():

Expand Down Expand Up @@ -647,13 +659,26 @@ def create_short_preparation_pipe(params, params_template={},
fast_T2, "indiv_params")

# outputnode
data_preparation_pipe.connect(
fast_T1, "restored_image",
outputnode, "stereo_debiased_T1")

data_preparation_pipe.connect(
fast_T2, "restored_image",
outputnode, "stereo_debiased_T2")
if "use_T2" in params.keys():

data_preparation_pipe.connect(
fast_T1, "restored_image",
outputnode, "stereo_debiased_T2")

data_preparation_pipe.connect(
fast_T2, "restored_image",
outputnode, "stereo_debiased_T1")

else:

data_preparation_pipe.connect(
fast_T1, "restored_image",
outputnode, "stereo_debiased_T1")

data_preparation_pipe.connect(
fast_T2, "restored_image",
outputnode, "stereo_debiased_T2")

elif "itk_debias" in params:

Expand All @@ -663,7 +688,7 @@ def create_short_preparation_pipe(params, params_template={},
itk_debias_T1 = NodeParams(
interface=niu.Function(
input_names=["img_file"],
output_names=["cor_img_file", "bias_img_file"],
output_names=["cor_img_file", "bias_img_file", "mask_file"],
function=itk_debias),
params=parse_key(params, "itk_debias"),
name='itk_debias_T1')
Expand All @@ -681,7 +706,7 @@ def create_short_preparation_pipe(params, params_template={},
itk_debias_T2 = NodeParams(
interface=niu.Function(
input_names=["img_file"],
output_names=["cor_img_file", "bias_img_file"],
output_names=["cor_img_file", "bias_img_file", "mask_file"],
function=itk_debias),
params=parse_key(params, "itk_debias"),
name='itk_debias_T2')
Expand All @@ -696,34 +721,72 @@ def create_short_preparation_pipe(params, params_template={},
itk_debias_T2, "img_file")

# outputnode
data_preparation_pipe.connect(
itk_debias_T1, "cor_img_file",
outputnode, "stereo_debiased_T1")

data_preparation_pipe.connect(
itk_debias_T2, "cor_img_file",
outputnode, "stereo_debiased_T2")
if "use_T2" in params.keys():

else:
print("No debias will be performed before extract_pipe")
data_preparation_pipe.connect(
itk_debias_T1, "cor_img_file",
outputnode, "stereo_debiased_T2")

if "denoise" in params.keys():
data_preparation_pipe.connect(
denoise_T1, "output_image",
itk_debias_T2, "cor_img_file",
outputnode, "stereo_debiased_T1")

data_preparation_pipe.connect(
denoise_T2, "output_image",
outputnode, "stereo_debiased_T2")
else:

data_preparation_pipe.connect(
crop_aladin_pipe, "outputnode.stereo_T1",
itk_debias_T1, "cor_img_file",
outputnode, "stereo_debiased_T1")

data_preparation_pipe.connect(
apply_crop_aladin_T2, 'out_file',
itk_debias_T2, "cor_img_file",
outputnode, "stereo_debiased_T2")

else:
print("No debias will be performed before extract_pipe")

if "denoise" in params.keys():

if "use_T2" in params.keys():

data_preparation_pipe.connect(
denoise_T1, "output_image",
outputnode, "stereo_debiased_T2")

data_preparation_pipe.connect(
denoise_T2, "output_image",
outputnode, "stereo_debiased_T1")
else:

data_preparation_pipe.connect(
denoise_T1, "output_image",
outputnode, "stereo_debiased_T1")

data_preparation_pipe.connect(
denoise_T2, "output_image",
outputnode, "stereo_debiased_T2")

else:

if "use_T2" in params.keys():

data_preparation_pipe.connect(
crop_aladin_pipe, "outputnode.stereo_T1",
outputnode, "stereo_debiased_T2")

data_preparation_pipe.connect(
apply_crop_aladin_T2, 'out_file',
outputnode, "stereo_debiased_T1")
else:

data_preparation_pipe.connect(
crop_aladin_pipe, "outputnode.stereo_T1",
outputnode, "stereo_debiased_T1")

data_preparation_pipe.connect(
apply_crop_aladin_T2, 'out_file',
outputnode, "stereo_debiased_T2")

# resample T1 to higher dimension
if "pad_template" in params.keys():

Expand Down
20 changes: 10 additions & 10 deletions macapype/pipelines/segment.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -375,16 +375,6 @@ def create_segment_atropos_pipe(params={}, name="segment_atropos_pipe"):

seg_at.inputs.prior_weight = params["use_priors"]

# split dseg_mask
split_dseg_mask = pe.Node(
interface=niu.Function(input_names=["nii_file"],
output_names=["list_split_files"],
function=split_indexed_mask),
name="split_dseg_mask")

segment_pipe.connect(seg_at, 'segmented_file',
split_dseg_mask, "nii_file")

# on segmentation indexed mask (with labels)
outputnode = pe.Node(
niu.IdentityInterface(
Expand All @@ -396,6 +386,16 @@ def create_segment_atropos_pipe(params={}, name="segment_atropos_pipe"):
segment_pipe.connect(seg_at, 'segmented_file',
outputnode, 'segmented_file')

# split dseg_mask
split_dseg_mask = pe.Node(
interface=niu.Function(input_names=["nii_file"],
output_names=["list_split_files"],
function=split_indexed_mask),
name="split_dseg_mask")

segment_pipe.connect(seg_at, 'segmented_file',
split_dseg_mask, "nii_file")

if "tissue_dict" in params.keys():
tissue_dict = params["tissue_dict"]

Expand Down
Loading